Ret inhibitor for use in treating cancer having a ret alteration

ABSTRACT

Disclosed herein are methods for treating a subject afflicted with a cancer having an activating RET alteration by administering an effective amount of a selective RET inhibitor, e.g., Compound 1 or pharmaceutically acceptable salts thereof, including, e.g., administering an amount of 60 mg to 400 mg of the selective RET inhibitor once daily.

This application is a continuation of PCT/US2019/025655, filed Apr. 3,2019, which claims priority to U.S. Provisional Application No.62/652,284, filed Apr. 3, 2018, U.S. Provisional Application No.62/656,297, filed Apr. 11, 2018, U.S. Provisional Application No.62/657,605, filed Apr. 13, 2018, and U.S. Provisional Application No.62/741,683, filed Oct. 5, 2018, the contents of each of which areincorporated by reference herein in their entirety.

This disclosure relates to methods for treating a subject afflicted witha cancer having an activating RET alteration by administering aneffective amount of a selective RET inhibitor, i.e., a compound which isspecifically designed to selectively target one or more RET orRET-altered kinases. As used herein, the term “afflicted with a cancer”means having a cancer. Said another way, a subject afflicted with acancer has a cancer. More specifically, the methods described hereinrelate to treating a subject having a cancer characterized by anactivating RET alteration. In some embodiments, the selective RETinhibitor is Compound 1 or pharmaceutically acceptable salts thereof. Insome embodiments, the selective RET inhibitor is administered oncedaily. In some embodiments, the effective amount is 60 mg to 400 mg, 100mg to 400 mg, 300 mg, or 400 mg. In some embodiments, the effectiveamount is 60 mg to 400 mg, 100 mg to 400 mg, 300 mg, or 400 mgadministered once daily. In some embodiments, the cancer is aRET-altered solid tumor, a RET-altered non-small cell lung cancer, or aRET-altered thyroid cancer. In some embodiments, the cancer is a braincancer, wherein the brain cancer is associated with non-small cell lungcancer. This disclosure also relates to methods of treating RET-alteredcancers by administering a physiological effective dose of a selectiveRET inhibitor that produces a sustained down-regulation of at least oneeffect marker.

The receptor tyrosine kinase (RTK) RET, along with glial cellline-derived neurotrophic factors (GDNF) and GDNF family receptors-α(GFRoc), is required for the development, maturation, and maintenance ofseveral neural, neuroendocrine, and genitourinary tissue types. However,increasing evidence implicates aberrant activation of RET as a criticaldriver of tumor growth and proliferation across a broad number of solidtumors (Mulligan L M., Nat. Rev. Cancer. 14:173-186 (2014)). OncogenicRET activation occurs via gain of function mutation or RET generearrangement resulting in the production of a RET fusion protein withconstitutively active RET signaling that promotes ligand-independenttumor growth. Oncogenic RET activation was initially described inhereditary and sporadic thyroid cancers and subsequently in non-smallcell lung cancer (NSCLC).

Oncogenic RET rearrangements have been identified in 1-2% of NSCLC(Lipson, D. et al., Nat. Med. 18:382-384 (2012); Takeuchi, K. et al.,Nat. Med. 18:378-381 (2012); Stransky, N. et al., Nat. Commun. 5:4846(2014)). This generates a constitutively active kinase that promotestumorigenesis. As with anaplastic lymphoma kinase (ALK) and c-rosoncogene (ROS) 1-rearranged NSCLC, RET-rearranged NSCLC typically hasadenocarcinoma histology (though occasionally squamous) and occurs inyoung, non-smoking patients. Because diagnostic testing for RET is notstandard of care, RET-rearranged patients with advanced NSCLC aretreated per NCCN guidelines for epidermal growth factor receptor (EGFR-)and ALK-negative adenocarcinoma. This usually includes chemotherapy witha platinum doublet or more recently with a checkpoint inhibitor however,clinical response and overall survival specifically in RET-rearrangedNSCLC with these agents is not well understood. Subsequent therapybeyond chemotherapy and checkpoint inhibitors for refractory patientsper NCCN guidelines is best supportive care or clinical trial.

Initial case reports and single-arm studies with the multikinase RETinhibitors (MKIs) cabozantinib, vandetanib, sorafenib, and alectinib inpatients with known RET-rearranged NSCLC have demonstrated clinicalactivity, suggesting that RET may be a valid target in NSCLC. Althoughencouraging response rates (˜12%-60%) (Horiike A et al., Lung Cancer93:43-6 (March 2016); Lin J J et al., J Thorac Oncol. 11(11):2027-32(November 2016); Gautshi O et al., J Clin Oncol. 34 (suppl; abstr 9014)(2016)) have been observed in these early studies, duration of responseis typically less than a year. MKI treatment was associated withsignificant toxicity, requiring dose interruption and/or dosemodification, which likely limit exposures required to effectivelyinhibit RET.

Oncogenic RET activation is also associated with thyroid cancer. Thyroidcancer consists primarily of differentiated thyroid cancer (DTC; ˜90% ofcases), medullary thyroid cancer (MTC; ˜5% of cases), and anaplasticthyroid cancer (<5% of cases). DTC arises sporadically from thyroidfollicular cells and consists of papillary thyroid cancer (PTC) (˜80% ofall thyroid cancer cases) and follicular thyroid cancer. In contrast,MTC arises from parafollicular C cells and occurs in both hereditary andsporadic forms. Oncogenic RET activation has been implicated as a driverin both MTC and PTC.

Recurrent gene rearrangements involving RET and a dimerizationdomain-encoding gene have been identified in approximately 5%-20% ofsporadic papillary tumors in adults. Kinase-activating RET mutationsoccur in nearly all cases of hereditary MTC (87%-97%) (Machens A et al.,N Engl J Med 349:1517-25 (2003); Mulligan L M et al., Nature363(6428):458-60 (1993 Jun. 3); Mulligan L M et al., J Int Med.238(4):343-346 (1995)) and approximately 43%-65% of sporadic MTC (EliseiR. et al., J Clin Endocrinol Metab. 93:682-687 (2008); Moura M M et al.,British Journal of Cancer 100:1777-1783 (2009)). These RET mutationsoccur in the extracellular domain (primarily at the C634 position) whichpromote ligand-independent dimerization and activation of RET, andkinase domains mutations (primarily M918T, A883F or V804L/M) whichpromote RET auto-activation and consequent oncogenic signaling (Romei Cet al., Nat Rev Endocrinol. 12(4):192-202 (2016 April)).

Both PTC and MTC are treated with surgery when localized (Fagin J A &Wells S A Jr., N Engl J Med. 375(11):1054-67 (2016 Sep. 15)). Ablativetherapy with radioactive iodine (RAI) is effective in PTC patients withrecurrence; however, patients eventually become refractory to RAI. AsMTC arises from follicular C-cells, RAI is not effective. Once advanced,RAI-refractory PTC and MTC are poorly responsive to chemotherapy andsystemic treatment with a small molecule MM is the standard of care forboth. Sorafenib and lenvatinib are approved MKIs for progressive and/orsymptomatic RAI-refractory PTC. Cabozantinib and vandetanib are approvedMKIs for advanced MTC and are used regardless of RET mutational status.MKIs used to treat thyroid cancer have broad activity against manykinases (e.g., RAF, MET, EGFR, VEGFR1-3, PDGFR, RET and others), and areassociated with significant dermatologic, cardiovascular, andgastrointestinal side effects. Therefore, National Clinical PracticeGuidelines in Oncology from the National Comprehensive Cancer Network(available athaps://www.nccn.org/professionals/physician_gls/f_guidelines.asp)recommends careful monitoring and dose interruption and/or dosemodification for drug-related side effects with these agents. Forpatients with disease progression on MM therapy or MKI intolerance,there are no effective therapies and NCCN guidelines recommend clinicaltrial participation.

Given the strong genetic and preclinical evidence that activated RET isan oncogenic disease driver, the lack of selective RET inhibitorsavailable, and the poor prognosis of many patients with RET-alteredtumors, a need remains for identifying dosing amounts and schedules withthe appropriate safety, exposures, and tolerability for selective RETinhibitors for the treatment of RET-altered cancers.

Small molecule compounds that selectively inhibit RET are a desirablemeans for treating cancers having an activating RET alteration. Onesmall molecule is(1S,4R)—N—((S)-1-(6-(4-fluoro-1H-pyrazol-1-yl)pyridin-3-yl)ethyl)-1-methoxy-4-(4-methyl-6-((5-methyl-1H-pyrazol-3-yl)amino)pyrimidin-2-yl)cyclohexanecarboxamide(Compound 1). Compound 1 has the chemical structure:

In March 2017, Compound 1 (also known as BLU-667) entered Phase Iclinical trials in the United States for the treatment of patients withthyroid cancer, non-small cell lung cancer, and other advanced solidtumors (NCT03037385). WO 2017/079140, incorporated herein by reference,describes the synthesis of Compound 1 (Example Compound 130) and alsodiscloses the therapeutic activity of this molecule to inhibit,regulate, and/or modulate RET kinase (Assays, Example 10 on pp. 72-74).

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A, 1B, and 1C are a series of bar graphs which show the impact ofCompound 1 on expression of DUSP6 and SPRY4 in LC2/ad (FIG. 1A),MZ-CRC-1 (FIG. 1B), and TT (FIG. 1C) cells.

FIG. 2 is a bar graph which shows the sustained decrease in expressionof the MAPK target genes DUSP6 and SPRY4 in a KIF5B-RET NSCLC PDX model.

FIG. 3 is a graph which shows in vivo anti-tumor activity of Compound 1in a cabozantinib-resistant tumor model generated from an engineeredKIF5B-RET V804L cell line.

FIG. 4A is a graph which shows tumor size and levels of calcitonin andCEA (carcinoembryonic antigen) decrease over the course of treatmentwith Compound 1. The RET-mutant MTC patient (RET L629P,D631_R635DELINSG, V637R MTC) was treated with 60 mg once daily and thenreceived successive dose escalation up to 300 mg once daily. FIG. 4B isa CT scan of the same RET-mutant MTC patient of FIG. 4A at baseline(top) and after 8 weeks of Compound 1 treatment (bottom) demonstratingrapid reduction in tumor growth. FIG. 4C is a graph which shows tumorsize and the levels of calcitonin and CEA decrease in a patient with RETM918T-mutant MTC over the course of treatment with Compound 1 with 300mg once daily. FIG. 4D is a CT scan of the RET M918T-mutant patient ofFIG. 4C's tumor at baseline (top) and after 24 weeks of Compound 1treatment (bottom). FIG. 4E is a graph which shows ctDNA analysis of RETM918T levels in plasma from an MTC patient during treatment. Pre- andpost-treatment tumor biopsy revealed a 93% decrease in DUSP6 and 86%decrease in SPRY4 mRNA expression after 28 days of treatment withCompound 1.

FIG. 5A is a graph which shows lung tumor and KIF5B-RET and TP53 ctDNAreduction over the course of treatment with 200 mg once daily Compound1; FIG. 5B is a CT scan which illustrates tumor at baseline (top) andafter 32 weeks of Compound 1 treatment (bottom).

FIG. 6A is a graph which shows the mean plasma concentration (ng/mL) vs.time (h); FIG. 6B is a bar graph which shows the percent change frombaseline in mean gene expression levels of DUSP6 and SPRY4.

FIG. 7A is a bar graph which shows dose-dependent reduction in CEA inpatients measured on cycle 2, day 1. FIG. 7B is a bar graph which showsdose-dependent reduction in calcitonin in patients measured on cycle 2day 1.

FIG. 8 is a waterfall plot which shows maximum tumor reduction—sum ofdiameter change from baseline percent—from patients in the phase Iclinical study. Data cut-off: Apr. 6, 2018.

FIG. 9A is a brain CT scan at baseline prior to treatment withCompound 1. FIG. 9B is a brain CT scan after 8 weeks of treatment withCompound 1 treatment.

FIG. 10 is a chart which shows patient response rate in RET-alteredNSCLC. Data cut-off: Apr. 6, 2018.

FIG. 11A is a CT scan at baseline prior to treatment with Compound 1.FIG. 11B is a CT scan after 8 weeks of treatment with Compound 1. FIG.11C is a CT scan at baseline prior to treatment with Compound 1. FIG.11D is a CT scan after 8 weeks of treatment with Compound 1.

FIG. 12 is a graph which shows that the response rate in medullarythyroid cancer patients increases with dose and duration of therapy.Specifically, the graph shows the response rate for dosing Compound 1 at60 to 200 mg once daily and 300/400 mg once daily over a period of 8 to24+ weeks.

FIG. 13 is a CT scan at baseline (BSL) and after 5 months of treatmentwith Compound 1 at 400 mg once daily.

ABBREVIATIONS AND DEFINITIONS

The following abbreviations and terms have the indicated meansthroughout:

“Compound 1” is(1S,4R)—N—((S)-1-(6-(4-fluoro-1H-pyrazol-1-yl)pyridine-3-yl)ethyl)-1-methoxy-4-(4-methyl-6-((5-methyl-1H-pyrazol-3-yl)amino)pyrimidin-2-yl)cyclohexanecarboxamide

As used herein, “DOR” means duration of response.

As used herein, “PD” means progressive disease.

As used herein, “SD” means stable disease.

As used herein, “CR” means complete response.

As used herein, “ORR” means overall all response rate.

As used herein, “CBR” means clinical benefit rate.

As used herein, “PFS” means progression free survival.

As used herein, a “fusion” is a protein that results from a chromosomaltranslocation in which two genes are joined with an in-frame codingsequence and results in a chimeric protein. In some embodiments, afusion is a chromosomal translocation where the kinase domain of oneprotein fuses to a dimerization domain of another gene.

As used herein, a “RET-altered cancer” is a cancer having an activatingrearranged during transfection (RET) alteration, which drivestumorigenesis. Non-limiting examples of activating RET alterationsinclude mutations, fusions, and copy number variations.

As used herein, a “RET fusion” is a gene rearrangement. RETrearrangements create a fusion protein juxtaposing the RET kinase domainand a dimerization domain of another protein, creating a constitutivelyactivated dimer, which drives tumorigenesis.

As used herein, a “RET fusion protein” is the result of a generearrangement.

As used herein, a “RET activating mutation” means a mutation in RETkinase which promotes ligand-independent, constitutive RET kinaseactivation, which drives tumorigenesis. For example, RET mutations canoccur in the extracellular cysteine residues (e.g., C620R or C634R/W),which trigger aberrant receptor dimerization, or RET mutations can occurin the intracellular kinase domain.

As used herein, a “RET inhibitor” is a compound which inhibits theactivity of RET kinase. RET kinase is wild-type RET kinase and/or one ormore RET-altered kinases (e.g., RET fusion, RET mutation, or RET copynumber variation).

Examples of RET inhibitors include, but are not limited to, Compound 1,LOXO-292 (selpercatinib), cabozantinib, vandetanib, alectinib,sorafenib, levatinib, ponatinib, dovitinib, sunitinib, foretinib,sitravatinib, DS-5010 (BOS 172738), and RXDX-105.

In some embodiments, a RET inhibitor may also inhibit other kinases. Asused herein, a “multi-kinase RET inhibitor” is a compound which inhibitswild type RET kinase and inhibits at least one other kinase equally ormore potently than wild type RET kinase. Examples of multikinase RETinhibitors include: cabozantinib; vandetanib; alectinib; sorafenib;levatinib, ponatinib; dovitinib; sunitinib; foretinib; sitravatinib;DS-5010; and RXDX-105.

As used herein, the term “selective RET inhibitor” means a compoundwhich selectively inhibits RET kinase. RET kinase can include RET wildtype kinase and/or one or more RET-altered kinases (e.g., RET fusion,RET mutation, or RET copy number variation). A selective RET inhibitor'sinhibitory activity against RET kinase is more potent in terms of IC₅₀value (i.e., the IC₅₀ value is subnanomolar) when compared with itsinhibitory activity against many other kinases (e.g., KDR, VEGFR-2, ABL,EGFR, FGFR2, HER2, IGFIR, JAKI, KIT, MET, AKTI, MEKl). Potency can bemeasured using known biochemical assays. Examples of selective RETinhibitors include Compound 1 and selpercatinib.

As used herein, the term “subject” or “patient” refers to organisms tobe treated by the methods of the present disclosure. Such organismsinclude, but are not limited to, mammals (e.g., murines, simians,equines, bovines, porcines, canines, felines, and the like), and in someembodiments, humans

Many cancers have been linked to aberrant RET expression (Kato et al.,Clin. Cancer Res. 23(8):1988-97 (2017)). Non-limiting examples of“cancer” as used herein include lung cancer, head and neck cancer,gastrointestinal cancer, breast cancer, skin cancer, genitourinary tractcancer, gynecological cancer, hematological cancer, central nervoussystem (CNS) cancer, peripheral nervous system cancer, endometrialcancer, colorectal cancer, bone cancer, sarcoma, spitzoid neoplasm,adenosquamous carcinoma, pheochromocytoma (PCC), hepatocellularcarcinoma, multiple endocrine neoplasia (MEN2A and MEN2B), andinflammatory myofibroblastic tumor. For other examples, see NatureReviews Cancer 14:173-86 (2014).

Additional non-limiting examples of cancer include hemangiopericytoma,differentiated thyroid carcinoma, anaplastic thyroid carcinoma, lungcarcinosarcoma, ureter urothelial carcinoma, uterine carcinosarcoma,basal cell carcinoma, Merkel cell carcinoma, atypical lung carcinoma,fallopian tube adenocarcinoma, ovarian epithelial carcinoma, salivarygland adenocarcinoma, meningioma, duodenal adenocarcinoma, cervicaladenocarcinoma, adrenal carcinoma, gastroesophageal junction carcinoma,cutaneous squamous cell carcinoma, pancreatic ductal adenocarcinoma,prostate adenocarcinoma, esophageal adenocarcinoma, endometrialadenocarcinoma, ovarian serous carcinoma, carcinoma unknown primary,bladder urothelial (transition cell) carcinoma, lung squamous cellcarcinoma, colorectal adenocarcinoma, head and neck squamous cellcarcinoma, and gastric adenocarcinoma.

In some embodiments, the cancer is liver cholangiocarcinoma. In someembodiments, the cancer is duodenum adenocarcinoma. In some embodiments,the cancer is uterus endometrial adenocarcinoma endometrioid.

In some embodiments, MEN2A is associated with pheochromocytoma andparathyroid hyperplasia.

In some embodiments, MEN2B is associated with mucosal neuromas,pheochromocytomas, intestinal ganglioneuromas and marfanoid habitus.

In some embodiments, the lung cancer is chosen from small cell lungcancer (SCLC), lung adenocarcinoma, non-small cell lung cancer (NSCLC),bronchioles lung cell carcinoma, and mesothelioma. In some embodiments,the lung cancer is SCLC. In some embodiments, the lung cancer is NSCLC.

In some embodiments, the head and neck cancer is chosen from thyroidcancer and cancer of the salivary gland. In some embodiments, thethyroid cancer is chosen from papillary thyroid carcinoma (PTC),metastatic papillary thyroid cancer, medullary thyroid cancer (MTC),diffuse sclerosing variant of papillary thyroid cancer, and thyroidgland carcinoma. In some embodiments, the cancer is familial medullarythyroid cancer. In some embodiments, the thyroid cancer is PTC. In someembodiments, the thyroid cancer is MTC.

In some embodiments, the gastrointestinal cancer is chosen fromesophageal cancer, esophagogastric cancer, gastrointestinal stromaltumor (e.g., imatinib-resistant gastrointestinal stromal tumor), smallbowel cancer, diffuse gastric cancer, and ampullary carcinoma.

In some embodiments, the breast cancer is metastatic breast cancer. Insome embodiments, skin cancer is melanoma or non-melanoma.

In some embodiments, the genitourinary tract cancer is chosen from coloncancer, metastatic colon cancer, bladder cancer, renal cell carcinoma(RCC), prostate cancer, hepatobiliary cancer, intrahepatic bile ductcancer, adrenocortical carcinoma, pancreatic cancer, and pancreaticductal adenocarcinoma.

In some embodiments, the gynecological cancer is chosen from uterinesarcoma, germ cell tumor, cervical cancer, rectal cancer, testicularcancer, and ovarian cancer. In some embodiments, the hematologicalcancer is chosen from leukemia, primary myelofibrosis with secondaryacute myeloid leukemia, myelodysplasia (MDS), non-Hodgkin lymphoma,chronic myeloid leukemia, Philadelphia chromosome-positive acutelymphoblastic leukemia, and chronic myelomonocytic leukemia (CMML).

In some embodiments, the peripheral nervous system cancer isparaganglioma. In some embodiments, the endometrial cancer isendometrialadenocarcinoma. In some embodiments, the sarcoma is a soft tissuesarcoma.

In some embodiments, the central nervous system (CNS) cancer is chosenfrom brain cancer associated with lung cancer and glioma.

Lung cancer is known to spread to the brain in about 40 percent of casesin which a metastasis has occurred. With lung cancer, this is consideredstage 4 of the disease, and the average survival time with brainmetastases is usually less than a year. Lung cancers with metastases tothe brain have a relatively poor prognosis, e.g., chemotherapy drugs.Brain metastases are difficult to treat for many reasons. Often, by thetime the patient first exhibits symptoms, they already have multiplelesions. Brain metastases tend to be very aggressive. The brain has manydefenses to reduce the penetration of harmful substances. Specifically,the blood-brain-barrier prevents many medications, e.g., compounds fromentering the brain. Treatment options may damage surrounding normaltissue and have a significant impact on the quality of life. Inparticular, there is a need to provide compounds that can beadministered at a safe dose, with good tolerability, and which penetratethe brain for treatment of brain metastases.

In some embodiments, the cancer is brain metastasis associated with lungcancer.

In some embodiments, the cancer is a “RET-altered cancer,” which, asused herein, means the cancer has an activating RET alteration. In someembodiments, the RET-altered cancer has a RET mutation or a RET generearrangement. In some embodiments, the RET-altered cancer is aRET-altered solid tumor.

As used herein, the term “effective amount” refers to the amount of aselective RET inhibitor (e.g., Compound 1 or a pharmaceuticallyacceptable salt thereof) sufficient to effect beneficial or desiredresults. Beneficial or desired results may be a therapeutic benefit orresult or a physiological benefit or result. An effective amount can beadministered in one or more administrations, applications, or dosagesand is not intended to be limited to a specific formulation oradministration route.

As used herein, the term “therapeutically effective amount” refers tothe amount of a selective inhibitor (e.g., Compound 1 or apharmaceutically acceptable salt thereof) sufficient to effectbeneficial or desired therapeutic results in a subject. Atherapeutically effective amount can be administered to a subject inneed thereof in one or more administrations, applications, or dosagesand is not intended to be limited to a specific formulation oradministration route. In some embodiments, a therapeutically effectiveamount provides the desired safety, exposure, and tolerability.Selecting the therapeutically effective amount, i.e., the right dose foradministering a compound, is a required step in the development of apharmaceutical drug for clinical use. Without adequate information ondosage, it is not possible for doctors to prescribe a particular drug topatients. Therefore, determining the correct drug dosage is a keyquestion that can only be answered in clinical studies. If the dose andfrequency of administration that allows safe and predictableadministration cannot be identified, then the compound cannot be amedically useful or commercially viable pharmaceutical product.

As used herein, the term “physiologically effective amount” refers tothe amount of a selective inhibitor (e.g., Compound 1 or apharmaceutically acceptable salt thereof) sufficient to effectbeneficial or desired physiological result in a subject. A physiologicalresult may be a sustained down-regulation of at least one effect markerin the subject.

As used herein, the term “treating” includes any effect, e.g.,lessening, reducing, modulating, ameliorating, or eliminating, thatresults in the improvement of the condition, disease, disorder, and thelike, or ameliorating a symptom thereof.

As used herein, an “effect marker” means DUSP6 mRNA expression, SPRY4mRNA expression, CEA, calcitonin, KIF5B ctDNA or TP53 ctDNA.

Some example embodiments of the disclosure include the following:

1. A method of treating a subject afflicted with a cancer having anactivating rearranged during transfection (RET) alteration, the methodcomprising administering to the subject a therapeutically effectiveamount of 300 to 400 mg of Compound 1 or a pharmaceutically acceptablesalt thereof once daily.2. The method of embodiment 1, wherein the amount administered is 300mg.3. The method of embodiment 1 or 2, wherein the amount administered is400 mg.4. The method of any one of embodiments 1-3, wherein the cancer ischosen from papillary thyroid carcinoma (PTC), medullary thyroid cancer(MTC), pheochromocytoma (PCC), pancreatic ductal adenocarcinoma,multiple endocrine neoplasia (MEN2A and MEN2B), metastatic breastcancer, testicular cancer, small cell lung cancer, non-small cell lungcancer (NSCLC), chronic myelomonocytic leukemia (CMML), colorectalcancer, ovarian cancer, inflammatory myofibroblastic tumor, and cancerof the salivary gland.5. The method of any one of embodiments 1-3, wherein the cancer ischosen from esophageal cancer, skin cancer (non-melanoma), endometrialcancer, head and neck cancer, bladder cancer, prostate cancer,hematological cancer, leukemia, soft tissue sarcoma, renal cellcarcinoma (RCC), non-Hodgkin lymphoma, hepatobiliary cancer,adrenocortical carcinoma, myelodysplasia (MDS), uterine sarcoma, germcell tumor, cervical cancer, central nervous system cancer, bone cancer,ampullary carcinoma, gastrointestinal stromal tumor, small bowel cancer,mesothelioma, rectal cancer, paraganglioma, and intrahepatic bile ductcancer.6. The method of any one of embodiments 1-3, wherein the cancer ischosen from adenocarcinoma, spitzoid neoplasm, lung adenocarcinoma,adenosquamous carcinoma, colon cancer, metastatic colon cancer,metastatic papillary thyroid cancer, diffuse sclerosing variant ofpapillary thyroid cancer, primary myelofibrosis with secondary acutemyeloid leukemia, diffuse gastric cancer, thyroid gland carcinoma, andbronchioles lung cell carcinoma.7. The method of any one of embodiments 1-3, wherein the cancer ischosen from hepatobiliary cancer, ampullary carcinoma, small bowelcancer, intrahepatic bile duct cancer, metastatic colon cancer, braincancer associated with lung cancer, brain metastasis associated withlung cancer, and retropentoneal paraganglioma.8. The method of any one of embodiments 1-3, wherein the cancer ischosen from medullary thyroid cancer (MTC) and non-small cell lungcancer (NSCLC).9. The method of embodiment 8, wherein the cancer is chosen fromsporadic MTC, metastatic RET-altered NSCLC, tyrosine kinase inhibitor(TKI)-refractory KIF5B-RET NSCLC, and KIF5B-RET NSCLC.10. The method of any one of embodiments 1-3, wherein the cancer ischosen from a brain cancer associated with a lung cancer.11. The method of embodiment 10, wherein the brain cancer is brainmetastasis.12. The method of any one of embodiments 1-11, wherein the activatingRET alteration comprises a RET mutation or a RET gene rearrangement(fusion).13. The method of any one of embodiments 1-11, wherein the activatingRET alteration is a RET mutation.14. The method of embodiment 12 or 13, wherein the RET mutation is apoint mutation.15. The method of any one of embodiments 12-14, wherein the RET mutationis a resistance mutation.16. The method of any one of embodiments 12-15, wherein the RETalteration is a RET mutation chosen from Table 1.17. The method of any one of embodiments 12-16, wherein the RET mutationis V804M, M918T, C634R, or C634W.18. The method of any one of embodiments 1-4, 8, 9, and 12-16, whereinthe cancer is RET-altered medullary thyroid cancer (MTC).19. The method of embodiment 18, wherein the cancer is familial MTC.20. The method of embodiment 18, wherein the cancer is sporadic MTC.21. The method of any one of embodiments 1-3 and 12-19, wherein thecancer is MTC having a M918T mutation.22. The method of any one of embodiments 1-3 and 12-19, wherein thecancer is MTC having a C634R mutation.

23. The method of any one of embodiments 1-3 and 12-19, wherein thecancer is MTC having a V804M mutation.

24. The method of any one of embodiments 1-3, 6, and 12-16, wherein thecancer is paraganglioma.25. The method of embodiment 24, wherein the cancer is retropentonealparaganglioma.26. The method of any one of embodiments 1-3, 6, 12-16, 24, and 25,wherein the paraganglioma has a R77H mutation.27. The method of any one of embodiments 1-11, wherein the activatingRET alteration is a gene-rearrangement (fusion).28. The method of embodiment 27, wherein the activating RET alterationis a fusion with a RET fusion partner chosen from Table 2.29. The method of embodiment 27 or 28, wherein the fusion is KIF5B-RET,CCDC6-RET, KIAA1468-RET, or NCOA4-RET.30. The method of any one of embodiments 1-4 and 27-29, wherein thecancer is RET-altered NSCLC.31. The method of embodiment 30, wherein the cancer is NSCLC having aKIF5B-RET fusion.32. The method of embodiment 30, wherein the cancer is NSCLC having aCCDC6-RET fusion.33. The method of embodiment 30, wherein the cancer is NSCLC having aKIAA1468-RET fusion.34. The method of embodiment 30, wherein the cancer is NSCLC having aRET fusion identified as FISH positive.35. The method of embodiment 29 or 30, wherein the RET alteration isKIF5B-RET V804L (cabozantinib resistant).36. The method of embodiment 29 or 30, wherein the RET alteration isCCDC6-RET V804M (ponatinib resistant).37. The method of any one of embodiments 1-4 and 27-29, wherein thecancer is RET-altered PTC.38. The method of embodiment 37, wherein the cancer is PTC having aCCDC6-RET fusion.39. The method of embodiment 37, wherein the cancer is PTC having aNCOA4-RET fusion.40. The method of any one of embodiments 1-3 and 27-29, wherein thecancer is RET-altered intrahepatic bile duct carcinoma.41. The method of embodiment 40, wherein the cancer is intrahepatic bileduct carcinoma having a NCOA4-RET fusion.42. The method of any one of embodiments 1-41, wherein the subject hasnot received prior treatment with a multikinase RET inhibitor.43. The method of any one of embodiments 1-41 wherein the subject hasreceived one or more prior treatments with a multikinase RET inhibitor.44. The method of embodiment 43, wherein the multikinase RET inhibitoris chosen from lenvatinib, vandetanib, cabozantinib, and RXDX-105.45. The method of any one of embodiments 1-41, wherein the subject hasnot received prior treatment with platinum.46. The method of any one of embodiments 1-41, wherein the subject hasreceived prior treatment with platinum.47. The method of any one of embodiments 1-41, wherein the subject hasreceived prior treatment with a selective RET inhibitor.48. The method of any one of embodiments 1-47, wherein the subject hasnot received prior chemotherapy.49. The method of any one of embodiments 1-47, wherein the subject hasreceived prior chemotherapy.50. The method of embodiment 49, wherein the prior chemotherapy ischosen from carboplatin, pemetrexed, abraxane, cisplatin, bevacizumab,and combinations thereof.51. The method of any one of embodiments 1-42, wherein the subject hasnot received prior immunotherapy.52. The method of any one of embodiments 1-42, wherein the subject hasreceived prior immunotherapy.53. The method of embodiment 52, wherein the prior immunotherapy ischosen from ipilimumab, pembrolizumab, nivolumab, MPDL3280A, MEDI4736,and combinations thereof.54. A method of treating a subject afflicted with a brain cancerassociated with a RET-altered lung cancer, the method comprisingadministering to the subject a therapeutically effective amount ofCompound 1 or a pharmaceutically acceptable salt thereof.55. The method of embodiment 54, wherein the brain cancer is brainmetastasis.56. A method of treating a subject afflicted with a cancer having anactivating RET mutation, the comprising administering to the subject aphysiologically effective amount of a RET inhibitor, whereinadministration of the RET inhibitor is associated with a sustaineddown-regulation of at least one effect marker in the subject.57. The method of embodiment 56, wherein the RET inhibitor is orallyadministered.58. The method of embodiment 56 or 57, wherein the RET inhibitor isCompound 1 or a pharmaceutically acceptable salt thereof.59. The method of any one of embodiments 56-58, wherein the effectmarker is chosen from DUSP6 mRNA expression, SPRY4 mRNA expression,carcinoembryonic antigen level, and calcitonin level.60. The method of any one of embodiments 56-58, wherein the effectmarker is KIF5B ctDNA level or TP53 ctDNA level.61. The method of any one of embodiments 56-59, wherein the amountadministered to the subject produces a greater than 95% down-regulationof at least one effect marker.62. The method of any one of embodiments 56-59, wherein the amountadministered to the subject produces a greater than 94%, greater than93%, greater than 92%, greater than 91%, greater than 90%, greater than89%, greater than 88%, greater than 87%, greater than 86% greater than85%, greater than 80%, greater than 75%, greater than 70%, greater than65%, greater than 60%, greater than 55%, or greater than 50%down-regulation in at least one effect marker.63. The method of embodiment 61, wherein the amount administered to thesubject produces a greater than 89%, greater than 88%, greater than 87%,greater than 86%, greater than 85%, greater than 80%, greater than 75%,or greater than 70% down-regulation in at least one effect marker.64. The method of any one of embodiments 56-59, wherein at least twoeffect markers are down-regulated.

TABLE 1 RET Point Mutations. Example RET Point Mutation Example RETPoint Mutation Amino acid position 2 Amino acid position 665 (e.g.,H665Q) Amino acid position 3 Amino acid position 666 (e.g., K666E,K666M, or K666N) Amino acid position 4 Amino acid position 686 (e.g.,S686N) Amino acid position 5 Amino acid position 691 (e.g., G691S) Aminoacid position 6 Amino acid position 694 (e.g., R694Q) Amino acidposition 7 Amino acid position 700 (e.g., M700L) Amino acid position 8Amino acid position 706 (e.g., V706M or V706A) Amino acid position 11Amino acid position 713 splice variant (e.g., E713K) Amino acid position12 Amino acid position 736 (e.g., G736R) Amino acid position 13 Aminoacid position 748 (e.g., G748C) Amino acid position 20 Amino acidposition 750 (e.g., A750P) Amino acid position 32 (e.g., S32L) Aminoacid position 765 (e.g., S765P) Amino acid position 34 (e.g., D34S)Amino acid position 766 (e.g., P766S or P766M6) Amino acid position 40(e.g., L40P) Amino acid position 768 (e.g., E768Q or E768D) Amino acidposition 64 (e.g., P64L) Amino acid position 769 (e.g., L769L) Aminoacid position 67 (e.g., R67H) Amino acid position 770 (e.g., R770Q)Amino acid position 114 (e.g., R114H) Amino acid position 771 (e.g.,D771N) Amino acid position 136 (e.g., glutamic Amino acid position 777(e.g., N777S) acid to stop codon) Amino acid position 145 (e.g., V145G)Amino acid position 778 (e.g., V778I) Amino acid position 180 (e.g.,arginine Amino acid position 781 (e.g., Q781R) to stop codon) Amino acidposition 200 Amino acid position 790 (e.g., L790F) Amino acid position292 (e.g., V292M) Amino acid position 791 (e.g., Y791F or Y791N) Aminoacid position 294 Amino acid position 802 Amino acid position 321 (e.g.,G321R) Amino acid position 804 (e.g., V804L, V804M, V804M, or V804E)Amino acid position 330 (e.g., R330Q) Amino acid position 805 (e.g.,E805K) Amino acid position 338 (e.g., T338I) Amino acid position 806(e.g., E806C, Y806E, Y806F, Y806S, Y806G, Y806H, Y806N, or Y806C) Aminoacid position 360 (e.g., R360W) Amino acid position 818 (e.g., E818K)Amino acid position 373 (e.g., alanine Amino acid position 819 (e.g.,S8191) to frameshift) Amino acid position 388 (e.g., V388A) Amino acidposition 393 (e.g., F393L) Amino acid position 823 (e.g., G823E) Aminoacid position 432 Amino acid position 826 (e.g., Y826M) Δ Amino acidresidues 505-506 (6-Base Amino acid position 833 (e.g., R833C) PairIn-Frame Germline Deletion in Exon 7) Amino acid position 510 (e.g.,A510V) Amino acid position 841 (e.g., P841L or P841P) Amino acidposition 511 (e.g., E511K) Amino acid position 843 (e.g., E843D) Aminoacid position 513 (e.g., A513D) Amino acid position 844 (e.g., R844W,R844Q, or R844L) Amino acid position 515 (e.g., C515S, Amino acidposition 848 (e.g., M848T) C515W) Amino acid position 525 (e.g., R525W)Amino acid position 852 (e.g., 1852M) Amino acid position 531 (e.g.,C531R, Amino acid position 866 (e.g., A866W) or 9 base pair duplication)Amino acid position 532 (e.g., Amino acid position 873 (e.g., R873W)duplication) Amino acid position 533 (e.g., G533C Amino acid position876 (e.g., A876V) or G533S) Amino acid position 550 (e.g., G550E) Aminoacid position 881 (e.g., L881V) Amino acid position 591 (e.g., V591I)Amino acid position 882 Amino acid position 593 (e.g., G593E) Amino acidposition 883 (e.g., A883F, A883S, A883T, or A883T*) Amino acid position600 (e.g., R600Q) Amino acid position 884 (e.g., E884K) Amino acidposition 602 (e.g., I602V) Amino acid position 886 (e.g., R886W) Aminoacid position 603 (e.g., K603Q Amino acid position 891 (e.g., S891A) orK603E2) Amino acid position 606 (e.g., Y606C) Amino acid position 897(e.g., R897Q) Amino acid position 609 (e.g., C609Y, Amino acid position898 (e.g., D898V) C609S, C609G, C609R, C609F, or C609W) Amino acidposition 611 (e.g., C611R, Amino acid position 901 (e.g., E901K) C611S,C611G, C611Y, C611F, or C611W) Amino acid position 618 (e.g., C618S,Amino acid position 904 (e.g., S904F C618Y, C618R, C618Y, C618G, C618F,C618W) or S904C2) Amino acid position 619 (e.g., F619F) Amino acidposition 907 (e.g., K907E or K907M) Amino acid position 620 (e.g.,C620S, Amino acid position 908 (e.g., R908K) C620W, C620R, C620G, C620L,C620Y, C620F) Amino acid position 623 (e.g., E623K) Amino acid position911 (e.g., G911D) Amino acid position 624 (e.g., D624N) Amino acidposition 912 (e.g., R912P, R912Q) Amino acid position 629 (e.g., L629P)Amino acid position 630 (e.g., C630A, Amino acid position 918 (e.g.,M918T, C630R, C630S, C630Y, or C630F) M918V, or M918L6) Amino acidposition 631 (e.g., D631N, Amino acid position 919 (e.g., A919V) D631Y,D631A, D631G, D631V, or D631E, D631_R635DELINSG) Amino acid position 632(e.g., E632K Amino acid position 921 (e.g., E921K) or E632G5) Δ Aminoacid residues 632-633 (6-Base Amino acid position 922 (e.g., S922P PairIn-Frame Germline Deletion in Exon or S922Y) 11) Amino acid position 633(e.g., 9 base Amino acid position 930 (e.g., T930M) pair duplication)Amino acid position 634 (e.g., C634W, Amino acid position 961 (e.g.,F961L) C634Y, C634S, C634R, C634F, C634G, C634L, C634A, or C634T, or aninsertion ELCR2, or a 12 base pair duplication) Amino acid position 635(e.g., R635G) Amino acid position 972 (e.g., R972G) Amino acid position636 (e.g., T636P Amino acid position 982 (e.g., R982C) or T636M4) Aminoacid position 637 (e.g., V637R) Amino acid position 640 (e.g., A640G)Amino acid position 1009 (e.g., M1009V) Amino acid position 641 (e.g.,A641S Amino acid position 1017 (e.g., D1017N) or A641T8) Amino acidposition 648 (e.g., V6481) Amino acid position 1041 (e.g., V1041G) Aminoacid position 649 (e.g., S649L) Amino acid position 1064 (e.g., M1064T)Amino acid position 664 (e.g., A664D) RET + 3 Amino acid position 629(e.g., L629P) Amino acid position 637 (e.g., V637R)

Some of the RET point mutations in Table 1 are discussed in: U.S. PatentApplication Publication No. 2014/0272951; Krampitz et al., Cancer120:1920-31 (2014); Latteyer et al., J Clin. Endocrinol. Metab. 101(3):1016-22 (2016); Silva et al. Endocrine 49.2:366-72 (2015); Jovanovic etal., Prilozi 36(1):93-107 (2015); Qi et al., Oncotarget 6(32):33993-4003(2015); Kim et al. ACTA ENDOCRINOLOGICA-BUCHAREST 11.2, 189-194, (2015);Cecchirini et al. Oncogene, 14:2609-12 (1997); Karrasch et al., Eur.Thyroid J 5(1):73-77 (2016); Scollo et al., Endocr. J 63:87-91 (2016);and Wells et al., Thyroid 25:567-610 (2015).

R525W and A513D may act in combination with S891A to enhance oncogenicactivity.

TABLE 2 RET Fusions. RET fusion partner Exemplary cancers in which thefusion is found BCR Chronic Myelomonocytic Leukemia (CMML) CLIP 1Adenocarcinoma KIFSB NSCLC, Ovarian Cancer, Spitzoid Neoplasm; LungAdenocarcinoma, Adenosquamous Carcinomas CCDC6 NSCLC, Colon Cancer,Papillary Thyroid Cancer; Adenocarcinoma; Lung Adenocarcinoma;Metastatic Colorectal Cancer; Adenosquamous Carcinoma, Metastaticpapillary thyroid cancer PTClex9 Metastatic papillary thyroid cancerNCOA4 Papillary Thyroid Cancer, NSCLC, Colon Cancer, Salivary GlandCancer, Metastatic Colorectal Cancer; Lung Adenocarcinoma, AdenosquamousCarcinomas; Diffuse Sclerosing Variant of Papillary Thyroid CancerTRIM33 NSCLC, Papillary Thyroid Cancer ERC1 Papillary Thyroid Cancer,Breast Cancer FGFRIOP CMML, Primary Myelofibrosis with secondary AcuteMyeloid Leukemia MBD1 Papillary Thyroid Cancer RAB61P2 Papillary ThyroidCancer PRKAR1A Papillary Thyroid Cancer TRIM24 Papillary Thyroid CancerKTN1 Papillary Thyroid Cancer GOLGA5 Papillary Thyroid Cancer, SpitzoidNeoplasms HOOK3 Papillary Thyroid Cancer KIAA1468 Papillary ThyroidCancer, Lung Adenocarcinoma TRIM27 Papillary Thyroid Cancer AKAP13Papillary Thyroid Cancer FKBP15 Papillary Thyroid Cancer SPECC1LPapillary Thyroid Cancer, Thyroid Gland Carcinoma TBL1XR1 PapillaryThyroid Cancer, Thyroid Gland Carcinoma CEP55 Diffuse Gastric CancerCUX1 Lung Adenocarcinoma ACBD5 Papillary Thyroid Carcinoma MYH13Medullary Thyroid Carcinoma PIBF1 Bronchiolus Lung Cell CarcinomaKIAA1217 Papillary Thyroid Cancer, Lung Adenocarcinoma, NSCLC MPRIPNSCLC

Some of the RET fusions in Table 2 are discussed in: Grubbs et al., JClin Endocrinol Metab, 100:788-93 (2015); Halkova et al., HumanPathology 46:1962-69 (2015); U.S. Pat. Nos. 9,297,011; 9,216,172; LeRolle et al., Oncotarget 6(30):28929-37 (2015); Antonescu et al., Am JSurg Pathol 39(7):957-67 (2015); U.S. Patent Application Publication No.2015/0177246; U.S. Patent Application Publication No. 2015/0057335;Japanese Patent Application Publication No. 2015/109806A; Chinese PatentApplication Publication No. 105255927A; Fang, et al., Journal ofThoracic Oncology 11.2 (2016): S21-S22; European Patent ApplicationPublication No. EP3037547A1; Lee et al., Oncotarget DOI:10.18632/oncotarget.9137, e-published ahead of printing, 2016; Saito etal., Cancer Science 107:713-20 (2016); Pirker et al., Transl Lung CancerRes, 4(6):797-800 (2015); and Joung et al., Histopathology 69(1):45-53(2016).

A person of ordinary skill in the art may determine if a subjectpossesses a RET-altered cell, cancer, gene, or gene product, e.g.,having a mutation, e.g., a fusion, deletion, insertion, translocation,frameshift, duplication, point mutation, and/or rearrangement, e.g.,using a method selected from hybridization-based methods,amplification-based methods, microarray analysis, flow cytometryanalysis, DNA sequencing, next-generation sequencing (NGS), primerextension, PCR, in situ hybridization, fluorescent in situhybridization, dot blot, and Southern blot.

To detect a fusion, primary tumor samples may be collected from asubject. The samples are processed, the nucleic acids are isolated usingtechniques known in the art, then the nucleic acids are sequenced usingmethods known in the art. Sequences are then mapped to individual exons,and measures of transcriptional expression (such as RPKM, or reads perkilobase per million reads mapped), are quantified. Raw sequences andexon array data are available from sources such as TCGA, ICGC, and theNCBI Gene Expression Omnibus (GEO). For a given sample, individual exoncoordinates are annotated with gene identifier information, and exonsbelonging to kinase domains are flagged. The exon levels are thenz-score normalized across all tumors samples.

Next, genes in which 5′ exons are expressed at significantly differentlevels than 3′ exons are identified. A sliding frame is used to identifythe breakpoint within an individual sample. Specifically, at eachiteration, an incremental breakpoint divides the gene into 5′ and 3′regions, and a t-statistic is used to measure the difference inexpression (if any) between the two regions. The breakpoint with themaximal t-statistic is chosen as the likely fusion breakpoint. As usedherein, “breakpoint” is the boundary at which two different genes arefused. It is sometimes referred to as a “fusion point.” The locationwhere the difference in exon expression is maximal between 5′ and 3′ isthe inferred breakpoint of the fusion. Thousands of tumor samples can berapidly profiled in this manner, generating a list of fusion candidates(ranked by t-statistic). High-ranking candidates can then be validated,and fusion partners identified by examining the raw RNA-seq data sets,and identifying chimeric pairs and/or split reads which support thefusion. Candidate fusions can then be experimentally confirmed asdescribed below.

Alternatively, the methods described in Wang L et al., Genes ChromosomesCancer 51(2):127-39 (2012). doi: 10.1002/gcc.20937, Epub 2011 Oct. 27;and Suehara Y et al., Clin Cancer Res. 18(24):6599-608 (2012). doi:10.1158/1078-0432.CCR-12-0838, Epub 2012 Oct. 10 can also be used.

It has been proposed that the inclusion of a pharmacodynamic assessmentof molecularly targeted therapies in clinical trials can streamline thedrug development process (Tan D S et al., Cancer J 15(5):406-20 (2009);Sarker D & Workman P. Adv Cancer Res 96:213-68 (2007)). Pharmacodynamicbiomarkers have been successfully utilized for the clinical developmentof kinase inhibitors, including imatinib and gefitinib (Sarker D &Workman P. Adv Cancer Res 96:213-68 (2007); Baselga J et al., J ClinOncol 23(23):5323-33 (2005); Druker B J et al., N Engl J Med344(14):1031-7 (2001)). As described herein, Compound 1 dose-dependentlyinhibited RET and SHC activation, which mirrored the inhibition of DUSP6and SPRY4 transcription across RET-driven preclinical models, indicatingthat these transcripts can serve as biomarkers for RET inhibitoryactivity. The translational capability of these markers was establishedin this study in which MTC tumor shrinkage induced by Compound 1treatment was associated with efficient inhibition of DUSP6 and SPRY4expression within the tumor tissue. To Applicant's knowledge, thisrepresents the first confirmation of RET target engagement by a smallmolecule inhibitor, multi-targeted or selective, within the clinicalsetting. These effect markers may be used to more precisely define theoptimal dose and schedule required for effective RET inhibition.

While it is possible for Compound 1 to be administered alone, in someembodiments, Compound 1 can be administered as a pharmaceuticalformulation, wherein Compound 1 is combined with one or morepharmaceutically acceptable excipients or carriers. Compound 1 may beformulated for administration in any convenient way for use in human orveterinary medicine. In certain embodiments, the compound included inthe pharmaceutical preparation may be active itself, or may be aprodrug, e.g., capable of being converted to an active compound in aphysiological setting.

The phrase “pharmaceutically acceptable” is employed herein to refer tothose compounds, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio.

Examples of pharmaceutically acceptable carriers include: (1) sugars,such as lactose, glucose, and sucrose; (2) starches, such as corn starchand potato starch; (3) cellulose and its derivatives, such as sodiumcarboxymethyl cellulose, ethyl cellulose, and cellulose acetate; (4)powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients,such as cocoa butter and suppository waxes; (9) oils, such as peanutoil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil, andsoybean oil; (10) glycols, such as propylene glycol; (11) polyols, suchas glycerin, sorbitol, mannitol, and polyethylene glycol; (12) esters,such as ethyl oleate and ethyl laurate; (13) agar; (14) bufferingagents, such as magnesium hydroxide and aluminum hydroxide; (15) alginicacid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer'ssolution; (19) ethyl alcohol; (20) phosphate buffer solutions; (21)cyclodextrins such as Captisol®; and (22) other non-toxic compatiblesubstances employed in pharmaceutical formulations.

Examples of pharmaceutically acceptable antioxidants include: (1) watersoluble antioxidants, such as ascorbic acid, cysteine hydrochloride,sodium bisulfate, sodium metabisulfite, sodium sulfite, and the like;(2) oil-soluble antioxidants, such as ascorbyl palmitate, butylatedhydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propylgallate, alpha-tocopherol, and the like; and (3) metal chelating agents,such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol,tartaric acid, phosphoric acid, and the like.

Solid dosage forms (e.g., capsules, tablets, pills, dragees, powders,granules, and the like) can include one or more pharmaceuticallyacceptable carriers, such as sodium citrate or dicalcium phosphate,and/or any of the following: (1) fillers or extenders, such as starches,lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders,such as, for example, carboxymethylcellulose, alginates, gelatin,polyvinyl pyrrolidone, sucrose, and/or acacia; (3) humectants, such asglycerol; (4) disintegrating agents, such as agar-agar, calciumcarbonate, potato or tapioca starch, alginic acid, certain silicates,and sodium carbonate; (5) solution retarding agents, such as paraffin;(6) absorption accelerators, such as quaternary ammonium compounds; (7)wetting agents, such as, for example, cetyl alcohol and glycerolmonostearate; (8) absorbents, such as kaolin and bentonite clay; (9)lubricants, such a talc, calcium stearate, magnesium stearate, solidpolyethylene glycols, sodium lauryl sulfate, and mixtures thereof; and(10) coloring agents.

Liquid dosage forms can include pharmaceutically acceptable emulsions,microemulsions, solutions, suspensions, syrups, and elixirs. In additionto the active ingredient, the liquid dosage forms may contain inertdiluents commonly used in the art, such as, for example, water or othersolvents, solubilizing agents and emulsifiers, such as ethyl alcohol,isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol,benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (inparticular, cottonseed, groundnut, corn, germ, olive, castor and sesameoils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols, andfatty acid esters of sorbitan, and mixtures thereof.

Suspensions, in addition to the active compounds, may contain suspendingagents as, for example, ethoxylated isostearyl alcohols, polyoxyethylenesorbitol and sorbitan esters, microcrystalline cellulose, aluminummetahydroxide, bentonite, agar-agar and tragacanth, and mixturesthereof.

Ointments, pastes, creams, and gels may contain, in addition to anactive compound, excipients, such as animal and vegetable fats, oils,waxes, paraffins, starch, tragacanth, cellulose derivatives,polyethylene glycols, silicones, bentonites, silicic acid, talc, andzinc oxide, or mixtures thereof.

Powders and sprays can contain, in addition to an active compound,excipients such as lactose, talc, silicic acid, aluminum hydroxide,calcium silicates, and polyamide powder, or mixtures of thesesubstances. Sprays can additionally contain customary propellants, suchas chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons,such as butane and propane.

Dosage forms for the topical or transdermal administration of Compound 1include powders, sprays, ointments, pastes, creams, lotions, gels,solutions, patches, and inhalants. The active compound may be mixedunder sterile conditions with a pharmaceutically acceptable carrier, andwith any preservatives, buffers, or propellants that may be required.

When Compound 1 is administered as a pharmaceutical, to humans andanimals, it can be given per se or as a pharmaceutical compositioncontaining, for example, 0.1 to 99.5% (such as 0.5 to 90%) of activeingredient in combination with a pharmaceutically acceptable carrier.

The formulations can be administered topically, orally, transdermally,rectally, vaginally, parentally, intranasally, intrapulmonary,intraocularly, intravenously, intramuscularly, intraarterially,intrathecally, intracapsularly, intradermally, intraperitoneally,subcutaneously, subcuticularly, or by inhalation.

The present disclosure is further illustrated by the following exampleswhich should not be construed as further limiting. The contents of allreferences cited throughout this application are expressly incorporatedherein by reference.

EXAMPLES Example 1: DUSP6 and SPRY4 Expression Analysis

Cells were treated with the indicated compounds for 7 hours before lysiswith Buffer RLT (QIAGEN, Hilden, Germany) containing 1%β-mercaptoethanol. Total RNA was isolated using the Rneasy Plus Mini kit(QIAGEN, Hilden, Germany) according to the manufacturer's instructions.First-strand cDNA was synthesized using the SuperScript VILO Master Mix(Thermo Fisher Scientific, Waltham, Mass.) according to themanufacturer's instructions. Real-time qPCR was run on ViiA 7 Real TimePCR System (Thermo Fisher Scientific). For qRT-PCR, the expression ofthe reference gene glucuronidase beta (GUSB) was used to normalizeexpression of the target genes DUSP6, SPRY4, and glycogen synthasekinase 3 beta (GSK3B). Replicate qRT-PCR reactions were analyzed foreach sample, and QuantStudio Real-Time PCR software (Life Technologies,Carlsbad, Calif.) normalized the average expression of DUSP6, SPRY4, orGSK3B to the average expression of the reference gene GUSB in eachsample. FIGS. 1A-1C show relative transcript expression of RET pathwaytargets DUSP6 and SPRY4 and AKT-pathway target GSK3B 7 hours aftertreatment of L2C/ad cells (FIG. 1A), MZ-CRC-1 cells (FIG. 1B), or TT MTCcells (FIG. 1C) with Compound 1 or cabozantinib. FIG. 2 shows relativetranscript expression of DUSP6, SPRY4 and GSK3B from KIF5B-RET NSCLCPDX. Tumors collected at the indicated times (hours) afteradministration of last dose. Data are the mean+SD. *P<0.05, **P<0.01,***P<0.001, 2-sided Student's t-test. SD, standard deviation.

Example 2: Generation of KIF5B-RET Ba/F3 Cells and ENU MutagenesisAssays

The DNA encoding the amino acid sequence of human KIF5B-RET variant 1was placed in a lentivirus vector under a doxycycline-inducible promoterto maximize expression with a carboxyl-terminal FLAG epitope tofacilitate immunodetection of the fusion by anti-FLAG antibodies.Lentiviral-mediated gene transduction was used to express KIF5B-RET inBa/F3 cells, KIF5B-RET dependent cells were selected by IL-3 withdrawaland confirmed to express the KIF5B-RET fusion protein by immunoblotanalysis. To generate Ba/F3 cells carrying V804 substitutions, WTKIF5B-RET Ba/F3 cells were mutagenized overnight with ENU and plated in96-well plates for a period of 2 weeks in the presence of 6concentrations of MKIs (ponatinib, regorafenib, cabozantinib, orvandetanib). The concentrations chosen ranged from 2×-64× theproliferation IC₅₀ for each compound: 125 nM to 4 μmol/L cabozantinib,20 to 640 nM ponatinib, and 250 nM to 8 μmol/L vandetanib. Genomic DNAwas isolated from resistant clones, and Sanger sequencing was used toidentify those that harbored substitutions. FIG. 3 shows antitumoractivity of Compound 1 compared with cabozantinib in KIF5B-RET V804LBa/F3 allografts.

Example 3: Phase I S tudy

A phase I, first-in-human study (NCT03037385) to define the maximumtolerated dose, safety profile, pharmacokinetics, and preliminaryanti-tumor activity of Compound 1 in advanced, RET-altered NSCLC, MTCand other solid tumors was initiated. Prior to study entry, writteninformed consent was obtained from all patients for treatment withCompound 1 and collection of blood and tumor samples for exploratorybiomarker analyses to characterize potential predictive biomarkers ofsafety and efficacy. Adult patients (>18 years of age) must have hadadvanced, unresectable solid tumors, with an Eastern CooperativeOncology Group performance status of 0 to 2, and adequate bone marrow,hepatic, renal, and cardiac function. Compound 1 was administeredorally, once daily, on a 4-week cycle using a Bayesian Optimal IntervalDesign. At dose levels>120 mg, documented RET-alteration wasadditionally required for study entry. Adverse events were graded perCommon Terminology Criteria for Adverse Events (CTCAE). Radiographicresponse by computed tomography was evaluated RECIST version 1.1(European Journal of Cancer 45: 228-247 (2009)). Levels of ctDNA inplasma were assessed using the PlasmaSELECT™-R64 NGS panel (PersonalGenome Diagnostics, Baltimore, Md.). Serum calcitonin levels in MTCpatients were measured by ELISA (Medpace, Cincinnati, Ohio). TumorDUSP6/SPRY4 levels were analyzed by qRT-PCR (Molecular MD, Portland,Oreg.).

Case Studies

Patient 1 was a 27-year-old patient with sporadic MTC harboring multipleRET mutations (L629P, D631_R635DELINSG, and V637R). The patient wastyrosine kinase inhibitor naïve prior to the start of Compound 1treatment with highly invasive disease that required emergenttracheostomy and extensive surgery, including total thyroidectomy,central neck dissection, bilateral levels 1 through 4 neck dissection,total thymectomy, and median sternotomy. The postoperative course wascomplicated by chylothorax. Multidisciplinary medical consensus wasagainst radiotherapy to the neck, and restaging scans showed leftparatracheal disease with tracheal and esophageal invasion as well asmetastatic disease to the lungs and liver. The two FDA approvedmulti-kinase drugs for MTC (vandetanib and cabozantinib) were notconsidered appropriate for this patient given the associated risk ofVEGFR-related toxicities that can include impaired wound healing, andincrease the risk of fistula formation and hemorrhage (CAPRELSA(vandetanib) [package insert]. Cambridge, Mass.: Sanofi Genzyme; 2016;COMETRIQ (cabozantinib) [package insert]. South San Francisco, Calif.:Exelixix, Inc.; 2018). Therefore, the patient was enrolled on theCompound 1 clinical trial and began treatment at the second dose level(60 mg, QD). Remarkably, after 28 days of Compound 1 therapy, there wasa >90% reduction in the serum tumor marker calcitonin (FIG. 4A). After 8weeks, target lesions were reduced by 19%. After successive doseescalations of Compound 1 to 200 mg QD, the patient achieved partialresponse with >30% tumor reduction per Response Evaluation Criteria inSolid Tumors (RECIST) version 1.1 (FIG. 4B). This patient subsequentlyescalated to 300 mg QD Compound 1 and achieved a confirmed partialresponse (47% maximal reduction) at 10 months. Overall, carcinoembryonicantigen (CEA) levels decreased by 57% over this period. Improved healthstatus with Compound 1 treatment allowed for removal of the patient'stracheostomy tube and a return to baseline body weight after severalkilograms of weight loss prior to treatment. Compound 1 has been welltolerated throughout 11 months of continuous treatment with the onlydrug-related adverse event being transient grade 1 decrease in whiteblood cells, which resolved without drug interruption or dosemodification. As of Apr. 13, 2018, the patient remains on therapy.

Patient 2 was a 56-year-old with sporadic RET M918T-mutant MTC, who hadresponded and then progressed on vandetanib, initiated therapy withCompound 1, 300 mg QD. Early signals of clinical activity emerged withinthe first few weeks of Compound 1 treatment: serum calcitonindecreased >90% and CEA decreased by 75% after 28 days (FIG. 4C). RETM918T circulating tumor DNA (ctDNA) decreased by 47% after 28 days andwas not detectable after 56 days. Paired tumor biopsies collectedpretreatment and 28 days post-treatment demonstrated a 93% reduction inDUSP6 and an 86% reduction in SPRY4 mRNA expression, confirmingRET-pathway inhibition within the tumor (FIG. 4E). Importantly, theseindications of activity were confirmed by radiographic response (−35%)per RECIST 1.1 after 8 weeks (FIG. 4D). The patient tolerated Compound 1treatment well without dose interruption; drug-related adverse eventswere grade 1 nausea and hyperphosphatemia. The patient continues ontherapy at 8 months with a confirmed partial response (maximum 47%reduction) as of Apr. 13, 2018.

Patient 3 was a 37-year-old patient with metastatic RET-altered NSCLC,who had progressed on cisplatin, pemetrexed, and bevacizumab, had tumortissue test positive for a RET fusion via FISH analysis. The patientinitiated treatment with 200 mg QD Compound 1, and ctDNA analysis atbaseline revealed a canonical KIF5B-RET fusion and co-occurring TP53mutation. Tumor reduction (−25%) was noted at first radiographicassessment after 8 weeks of treatment and correlated with a concomitantdecline in KIF5B-RET and TP53 ctDNA levels (FIG. 5A). The patientachieved a partial response on the second radiographic assessment after16 weeks (FIG. 5B) and continues on treatment through 10 months with aconfirmed partial response as of Apr. 13, 2018. As observed with the MTCpatients described above, Compound 1 has been well tolerated, with alldrug-related adverse events being grade 1 and including constipation(resolved), dry skin, rash, and leukopenia.

Patient 4 was a 69-year-old patient with NSCLC, who had prior lungresection nephrectomy, and pleural drainage. The patient initiatedtreatment with 400 mg QD Compound 1. Tumor reduction was noted againstKIF5B-RET NSCLC brain metastases (FIG. 9). Specifically, evidence ofintracranial anti-tumor activity was observed in the patient. Atbaseline, the patient had an approximately 6 mm metastatic lesion in thebrain, which appeared to resolve after 8 weeks on treatment. At the timeof the 8-week assessment, the patient was determined to have stabledisease.

Patient 5 was a 74-year-old former smoker with locally advancedKIF5B-RET NSCLC. The patient's CT scans are shown in FIGS. 11A-11D. Thepatient had received concurrent chemoradiation with cisplatin andpemetrexed, was then treated with carboplatin and nab-paclitaxel andeventually progressed. Next generation sequencing of the tumor tissue,along with FISH, revealed a KIF5B-RET fusion, and the patient wasenrolled on a clinical trial testing a combination regimen of vandetaniband everolimus (NCT01582191). The patient achieved a partial response,but restaging scans performed after 11 cycles showed progressivedisease, which was associated with clinical symptoms of increasingdyspnea and worsening performance status. The patient was then enrolledon the phase 1 trial of Compound 1. After 16 weeks of treatment withCompound 1 (300 mg QD), the patient had a partial response with 34%reduction of tumor volume (FIGS. 11C and 11D) and improvement of dyspneaand performance status. Compound 1 has been well tolerated throughouttreatment, and the patient has not experienced drug-related adverseevents as of Apr. 13, 2018.

Patient 6 was a 23-year old woman with PTC, sclerosing variant(CCDC6-RET fusion), who presented 6 years ago with symptomatic diffuselung metastases requiring supplemental oxygen, since diagnosis. She hadprogressed on sorafenib and lenvatinib. She initiated treatment withCompound 1 at 400 mg once daily. FIG. 13 shows tumor reduction after 5months of treatment with Compound 1. Within 5 months, she was weaned toroom air.

Measuring ctDNA Levels

Levels of one example effect marker, ctDNA in plasma (e.g., KIF5B orTP53 ctDNA), may be assessed using the PlasmaSELECT™-R64 NGS panel(Personal Genome Diagnostics, Baltimore, Md.). PlasmaSELECT™ 64 analyzescirculating tumor DNA for genetic alterations in cancer. Specifically,PlasmaSELECT™ 64 evaluates a targeted panel of 64 well-characterizedcancer genes. Cell-free DNA is extracted from plasma and prepared usingproprietary methods that accommodate low abundance sample DNA. Samplesare then processed using a proprietary capture process and high coveragenext-generation sequencing.

Steady State Plasma Concentration, RET IC₉₀ and Brain IC₉₀ (Predicted)

Blood samples were collected at pre-determined time points from patientsdosed with 30 to 600 mg Compound 1 orally once daily. Plasma sampleswere analyzed for Compound 1 using a validated liquidchromatography-tandem mass spectrometry (LC-MS/MS) method. The plasmaCompound 1 concentration-time data were graphed using Phoenix WinNonlin©(Version 6.4, Certara L. P.) or Graphpad Prism (Version 7.02). FIG. 6Ashows the plasma concentration-time profile of Compound 1 at steadystate. The RET IC₉₀ and brain IC₉₀ (predicted) are based on projectionsand extrapolations based on PK and PD data in animals.

A twice a day (BID) dosing schedule was also explored as part of thephase I clinical trial. The BID dosing schedule started at a 300 mgtotal daily dose (200 mg in the morning, 100 mg in the evening). A totalof 9 patients were enrolled into the BID dose escalation: 4 patients at300 mg total daily dose (200 mg in the morning, 100 mg in the evening)and 5 patients at 200 mg total daily dose (100 mg BID). Of the first 4patients enrolled at the 300 mg total daily dose, 2 patients experienceddose limiting toxicities (DLTs) of Grade 3 hypertension and the dose wassubsequently de-escalated to 100 mg BID. Two of 5 patients at 100 mg BIDexperienced DLTs, including 1 patient with Grade 3 hypertension and 1patient with Grade 3 tumor lysis syndrome. Based on overall safety,exposure, and tolerability, QD was the superior dosing schedule andchosen for the dose expansion.

All publications and patents mentioned herein are hereby incorporated byreference in their entirety.

1.-21. (canceled)
 22. A method of treating a subject with a rearrangedduring transfection RET-altered thyroid cancer, comprising orallyadministering to the subject with the RET-altered thyroid cancer oncedaily 100 mg to 400 mg of Compound 1, wherein Compound 1 is:


23. The method of claim 22, wherein the RET-altered thyroid cancer has aRET fusion.
 24. The method of claim 23, wherein the RET fusion isselected from the group consisting of CCDC6-RET, PTClex9-RET, NCOA4-RET,TRIM33-RET, ERC1-RET, MBD1-RET, RAB61P2-RET, PRKAR1A-RET, TRIM24-RET,KTN1-RET, GOLGA5-RET, HOOK3-RET, KIAA1468-RET, TRIM27-RET, AKAP13-RET,FKBP15-RET, SPECC1L-RET, TBL1XR1-RET, ACBD5-RET, KIAA1217-RET, andMYH13-RET.
 25. The method of claim 22, wherein the RET-altered thyroidcancer has a RET mutation.
 26. The method of claim 25, wherein the RETmutation is V804L, V804M, or V804E.
 27. The method of claim 25, whereinthe RET mutation is M918T.
 28. The method of claim 25, wherein the RETmutation is C609Y, C609S, C609G, C609R, C609F, C609W, C611R, C611S,C611G, C611Y, C611F, C611W, C618S, C618Y, C618R, C618Y, C618G, C618F,C618W, C620S, C620W, C620R, C620G, C620L, C620Y, C620F, C630A, C630R,C630S, C630Y, C630F, C634W, C634Y, C634S, C634F, C634G, C634L, C634A, orC634T.
 29. The method of claim 25, wherein the RET mutation is L709F.30. The method of claim 25, wherein the RET mutation is R844W, R844Q, orR844L.
 31. The method of claim 25, wherein the RET mutation is A883F,A883S, or A883T.
 32. The method of claim 25, wherein the RET mutation isK666E, K666E, K666M, or K666N.
 33. The method of claim 22, wherein theRET-altered thyroid cancer is papillary thyroid cancer.
 34. The methodof claim 22, wherein the thyroid cancer is radioactive iodine (RAI)refractory.
 35. The method of claim 22, wherein the subject is orallyadministered 100 mg of Compound 1 once daily.
 36. The method of claim22, wherein the subject is orally administered 300 mg of Compound 1 oncedaily.
 37. The method of claim 22, wherein the subject is orallyadministered 400 mg of Compound 1 once daily.
 38. A method of treating asubject with a rearranged during transfection RET mutant medullarythyroid cancer (MTC), comprising orally administering to the subjectwith the RET mutant MTC once daily 100 mg to 400 mg of Compound 1,wherein Compound 1 is:


39. A method of treating a subject with a rearranged during transfectionRET-altered thyroid cancer, comprising orally administering once dailyto the subject with the RET-altered thyroid cancer one or more soliddosage forms each comprising a pharmaceutically acceptable excipient and100 mg of Compound 1 or a pharmaceutically acceptable salt thereof,wherein Compound 1 is:


40. A method of treating a subject with a rearranged during transfectionRET mutant medullary thyroid cancer (MTC), comprising orallyadministering once daily to the subject with the RET mutant medullarythyroid cancer (MTC) one or more solid dosage forms each comprising apharmaceutically acceptable excipient and 100 mg of Compound 1 or apharmaceutically acceptable salt thereof, wherein Compound 1 is:


41. A method of treating a subject with a rearranged during transfectionRET fusion thyroid cancer, comprising orally administering to thesubject with the RET fusion thyroid cancer once daily 100 mg to 400 mgof Compound 1, wherein Compound 1 is:


42. A method of treating a subject with a rearranged during transfectionRET fusion thyroid cancer, comprising orally administering once daily tothe subject with the RET fusion thyroid cancer one or more solid dosageforms each comprising a pharmaceutically acceptable excipient and 100 mgCompound 1 or a pharmaceutically acceptable salt thereof, whereinCompound 1 is:


43. The method of claim 22, wherein the RET-altered thyroid cancer ismedullary thyroid cancer.
 44. The method of claim 22, wherein theRET-altered thyroid cancer is differentiated thyroid cancer.
 45. Themethod of claim 22, wherein the RET-altered thyroid cancer is follicularthyroid cancer.
 46. The method of claim 22, wherein the RET-alteredthyroid cancer is anaplastic thyroid cancer.